MolNFT v1 · #37309 · protein
Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a 16-residue peptide encompassing the 4E10 epitope on GP41
2FX7: “Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a 16-residue peptide encompassing the…”. X-ray diffraction, 4 pockets (best druggability 0.59). MolNFT v1 #37309 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2FX7
- Type
- protein
- Length
- 458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 4E10; Fragment of HIV glycoprotein (GP41)
- UniProt
- P05880
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab 4E10 | protein | 214 | 7% helix, 50% strand | — |
| H | Fab 4E10 | protein | 228 | 8% helix, 53% strand | — |
| P | Fragment of HIV glycoprotein (GP41) | protein | 16 | 88% helix, 0% strand | P05880 |
Ligands and binding sites
- GOL · Glycerol · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.59 | 0.74 | 64 | empty |
| 2 | 265 | 0.53 | 0.75 | 37 | empty |
| 3 | 104 | 0.42 | 0.77 | 18 | empty |
| 4 | 119 | 0.38 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1685 Ų buried · 13 hydrogen bonds · protein-protein
- H–P · 603 Ų buried · 4 hydrogen bonds · protein-protein
- L–P · 216 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2FX7 · Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a 16-residue… · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05880
- Elsewhere: RCSB PDB 2FX7 · PDBe 2FX7 · UniProt P05880
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